7BUS | pdb_00007bus

Chalcone synthase from Glycine max (L.) Merr (soybean)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DXA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	30% PEG4000, 0.2M ammonium acetate and 0.1M sodium citrate (pH 5.6)

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.76	α = 90
b = 98.94	β = 90
c = 159.29	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2019-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.00000	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.52	159.3	99.7	0.575	0.446	0.973	6.56	15.4		30056

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.52	2.67	99.9		4.306	4.459	0.201	1.08	13.88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6DXA	2.52	49.519	30007	1492	99.784	0.193	0.1894	0.2	0.2536	0.26	35.771

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-5.072			3.745		1.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.474
r_dihedral_angle_3_deg	17.534
r_dihedral_angle_4_deg	14.944
r_dihedral_angle_1_deg	7.399
r_lrange_it	6.145
r_lrange_other	6.13
r_scangle_it	4.095
r_scangle_other	4.092
r_mcangle_other	3.266
r_mcangle_it	3.265
r_scbond_it	2.426
r_scbond_other	2.419
r_mcbond_it	1.974
r_mcbond_other	1.971
r_angle_refined_deg	1.465
r_angle_other_deg	1.152
r_symmetry_xyhbond_nbd_refined	0.342
r_nbd_other	0.251
r_nbd_refined	0.199
r_symmetry_nbd_other	0.184
r_symmetry_nbd_refined	0.175
r_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.155
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.075
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5988
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XSCALE	data scaling
MOLREP	phasing